4A3M Transcription date Sep 30, 2011
title Rna Polymerase II Initial Transcribing Complex With A 4nt Dn Hybrid And Soaked With Ampcpp
authors A.C.M.Cheung, S.Sainsbury, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Fragment: Residues 1-1732
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rpb1, Rna II Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Rna Polymerase II Subunit 2, B150, Rpb2, Dna-Direc Polymerase II 140 Kda Polypeptide;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit 3, Rna Polymerase II Sub B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide, R

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, B32, Rpb4, Dna-Direc Polymerase II 32 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, II, And III 27 Kda Polypeptide,

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, II, And III 23 Kda Polypeptide,

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, B16, Rpb7

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 Abc14.5, Dna-Directed Rna Polymerases I, II, And III 14.5 K Polypeptide, Rpb8;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, B12.6, Rpb9, Dna-Dir Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme Subunit 9;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 Abc8, Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Rpb10;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, B13.6, Rpb11, Dna-D Rna Polymerase II 13.6 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Rpb12;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-D(Apapgptpapcptp)-3'
Chain: N
Synonym: Non Template Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-R(Apgpgpa)-3'
Chain: P
Synonym: Transcript Rna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-D(Apgpcptpcpapapgptpapcptptptp Tptpcpcpbrupgpgptpcpaptpt)-3';
Chain: T
Synonym: Template Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.154 R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.270 392.990 282.160 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.90 Å
ligand APC, BRU, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • B
  • RNA-directed 5'-3' RNA polym...


  • C
  • RNA-directed 5'-3' RNA polym...


  • D
  • RNA-directed 5'-3' RNA polym...


  • E
  • RNA-directed 5'-3' RNA polym...


  • F
  • RNA-directed 5'-3' RNA polym...


  • G
  • RNA-directed 5'-3' RNA polym...


  • H
  • RNA-directed 5'-3' RNA polym...


  • I
  • RNA-directed 5'-3' RNA polym...


  • J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
  • K
  • RNA-directed 5'-3' RNA polym...


  • L
  • RNA-directed 5'-3' RNA polym...


  • Primary referenceStructural basis of initial RNA polymerase II transcription., Cheung AC, Sainsbury S, Cramer P, EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1377 Kb) [Save to disk]
  • Biological Unit Coordinates (4a3m.pdb1.gz) 1362 Kb
  • LPC: Ligand-Protein Contacts for 4A3M
  • CSU: Contacts of Structural Units for 4A3M
  • Structure Factors (941 Kb)
  • Retrieve 4A3M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A3M from S2C, [Save to disk]
  • Re-refined 4a3m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A3M in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4A3M
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A3M, from MSDmotif at EBI
  • Fold representative 4a3m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a3m_D] [4a3m_F] [4a3m_N] [4a3m_G] [4a3m] [4a3m_A] [4a3m_P] [4a3m_I] [4a3m_K] [4a3m_B] [4a3m_J] [4a3m_T] [4a3m_E] [4a3m_C] [4a3m_H] [4a3m_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4A3M: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4A3M
  • Community annotation for 4A3M at PDBWiki (http://pdbwiki.org)
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